Hi Bhavani those files don't list the error. Please see:
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?highlight=%28reporting%29%7C%28error%29 for the information we need in order to be able to help you. cheers Bruce On Thu, 12 Feb 2015, Selvaraj, Bhavani wrote: > Hi > I tried running recon all command for two case study and it ended with error. > I am attaching the document. > Please could you help me solve this issue? > Thanks, > Bhavani > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu > [freesurfer-requ...@nmr.mgh.harvard.edu] > Sent: Thursday, February 12, 2015 12:00 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 132, Issue 15 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. updating from 5.0 to 5.3 (Aaron Goldman) > 2. Re: Interhemispheric registration of .mgh files (Bruce Fischl) > 3. Help: error on running dt_recon (Sampada Sinha) > 4. Re: Help: error on running dt_recon (Douglas Greve) > 5. Re: Interhemispheric registration of .mgh files (Douglas Greve) > 6. Re: Interhemispheric registration of .mgh files (Douglas Greve) > 7. Re: Different results for GLM analysis of parcellated regions > and vertex-wise analyses (Bronwyn Overs) > 8. Re: updating from 5.0 to 5.3 (Harms, Michael) > 9. Re: DTI question (Thomas Potrusil) > 10. Re: bbregister error [Was: TRACULA mask error] (Worker, Amanda) > 11. Re: Interhemispheric registration of .mgh files (Konrad Wagstyl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 11 Feb 2015 20:22:07 +0000 > From: Aaron Goldman <aaron.gold...@libd.org> > Subject: [Freesurfer] updating from 5.0 to 5.3 > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <D6503DE7F4AB474A8FFCE8BC36F0224820DD33@lieber-srv01.lieber.local> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I have a large set of images previously run in FreeSurfer 5.0. I'm also > preparing to run a new batch of images and debating whether to use 5.3 or > stick with 5.0. If I updated all the old datasets to 5.3, would I need to > visually QC them a second time, or are the versions similar enough that I can > rely on my pre-existing QC? Also, am I correct in assuming I shouldn't mix > versions 5.0 and 5.3? > > Thanks, > > Aaron > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_0db58b38_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=5UcMVLhP4c-5tlXlhqydtYme5fk9N_47Aap066BmpS0&e= > > ------------------------------ > > Message: 2 > Date: Wed, 11 Feb 2015 16:12:52 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Interhemispheric registration of .mgh files > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: "sophie.adler...@ucl.ac.uk" <sophie.adler...@ucl.ac.uk> > Message-ID: > <alpine.lrh.2.11.1502111612350.11...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Konrad > > you should be able to do this with mri_surf2surf, although the syntax > might be tricky. > > cheers > Bruce > On Mon, 9 Feb 2015, Konrad Wagstyl wrote: > >> Hi all, >> >> We're having some trouble using interhemispheric registration. It works fine >> for files that are automatically registered eg thickness, volume etc. but >> not for mgh files, like ?h.w-g.pct.mgh. >> Is there a way of adding files to xhemi/surf/ so that other surfaces files >> can be compared between hemispheres? >> >> Thanks, >> Konrad >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >> >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 11 Feb 2015 15:28:48 -0600 > From: Sampada Sinha <drsampadasi...@gmail.com> > Subject: [Freesurfer] Help: error on running dt_recon > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <9a4e12bd-543f-44d3-982f-ba06de5b8...@gmail.com> > Content-Type: text/plain; charset="windows-1252" > > Dear freesurfer experts, > > Sorry for posting such a long message but I am trying to run dt_recon command > on DTI images acquired in dicom format using 3T_Toshiba (Toshiba_MEC_MR3). > Image parameters are: Scanning sequence =Spin Echo; TR=9 ; TE=082.0 ; Flip > angle = 90; Slice thickness= 3.0000; acquisition matrix is 160. Howsoever, I > used many tools to get the bval and bvect gradient from the conversion of dcm > files to nifti but couldn't get one (dcm2nii, mricron). Even with freesurfer, > I am getting following error: (My dcm file is in directory: > /Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm) > I used following command to get the dt_recon work: > > Sampada$ export FREESURFER_HOME=/Applications/freesurfer > Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /Applications/fsl > Sampada$ tcsh > Sampada% cd /Users/sampada/Desktop/DTIDCM/Raw/ > ~/Desktop/DTIDCM/Raw] Sampada% setenv SUBJECTS_DIR > /Users/Sampada/Desktop/DTIDCM/Raw > ~/Desktop/DTIDCM/Raw] Sampada% set subj =Diff001 > ~/Desktop/DTIDCM/Raw] Sampada% dt_recon --i > /Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm --s $subj --o > /Users/Sampada/Desktop/DTIDCM/Raw > > Error Message: ERROR: Flag /Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm > unrecognized. > --i /Users/Sampada/Desktop/DTIDCM/Raw/I0005129.dcm > /Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm > /Users/Sampada/Desktop/DTIDCM/Raw/I0005131.dcm > /Users/Sampada/Desktop/DTIDCM/Raw/I0005132.dcm > /Users/Sampada/Desktop/DTIDCM/Raw/I0005133.dcm > /Users/Sampada/Desktop/DTIDCM/Raw/I0005134.dcm > and so on? (dt_recon exited with ERRORS at Wed Feb 11 01:47:01 CST 2015) > > Then I used nii converted file instead of the dcm file and it shows the > following error > > Sampada% dt_recon --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii --s > $subj --o /Users/Sampada/Desktop/DTIDCM/Raw > INFO: SUBJECTS_DIR is /Users/Sampada/Desktop/DTIDCM/Raw > dt_recon logfile > Wed Feb 11 15:02:47 CST 2015 > VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ > setenv SUBJECTS_DIR /Users/Sampada/Desktop/DTIDCM/Raw > cd /Users/Sampada/Desktop/DTIDCM/Raw > /Applications/freesurfer/bin/dt_recon --i > /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii --s Diff001 --o > /Users/Sampada/Desktop/DTIDCM/Raw > rmbp.home > Sampada > /Applications/fsl/bin/eddy_correct > ECRefTP 0 > #@#------------------------------- > Converting input > Wed Feb 11 15:02:47 CST 2015 > cd /Users/Sampada/Desktop/DTIDCM/Raw > mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii > /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii > mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii > /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii... > TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.994743, 0.0323186, 0.097165) > j_ras = (0.0525116, 0.97562, 0.21309) > k_ras = (0.0879093, -0.217072, 0.972189) > writing to /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii... > > > cd /Users/Sampada/Desktop/DTIDCM/Raw > mri_probedicom --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii > [rmbp:~/Desktop/DTIDCM/Raw] Sampada% > > I would be very grateful if I any response and know where I am going wrong. I > am also attaching the dt_recon.log file with this query. > > Much thanks for your time! > > Kind regards, > > Sampada > Post-Doctoral Associate > University of Minnesota (East Bank) > Molecular and neuroimaging laboratory > Department of Psychiatry > Minneapolis-55415 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_9853b0ff_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=TFoeAHvZwc_6Syi5Q-QLkuGYK5ueo_QtGjfoiPnzwsQ&e= > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: dt_recon.log > Type: application/octet-stream > Size: 1825 bytes > Desc: not available > Url : > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_9853b0ff_attachment.obj&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=BzMrGNe87ySviFedetbx-BdEpIyHPeAgFojZM8XN-4s&e= > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_9853b0ff_attachment-2D0001.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=R1Zds6pmLakBC82sGuyj6q9_Fc3nJX6-MAL0ZOCxrZo&e= > > ------------------------------ > > Message: 4 > Date: Wed, 11 Feb 2015 17:46:24 -0500 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Help: error on running dt_recon > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54dbdbc0.6030...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > > Just give it one of the dicoms (ie, don't use the "*" wild card, just > give it the actual file name of one of the files in the series, it will > find the rest) > doug > > On 2/11/15 4:28 PM, Sampada Sinha wrote: >> Dear freesurfer experts, >> >> Sorry for posting such a long message but I am trying to run dt_recon >> command on DTI images acquired in dicom format using 3T_Toshiba >> (Toshiba_MEC_MR3). Image parameters are: Scanning sequence =Spin Echo; >> TR=9 ; TE=082.0 ; Flip angle = 90; Slice thickness= 3.0000; >> acquisition matrix is 160. Howsoever, I used many tools to get the >> bval and bvect gr >> >> >> adient from the conversion of dcm files to nifti but couldn't get one >> (dcm2nii, mricron). Even with freesurfer, I am getting following >> error: (My dcm file is in directory: >> /Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm) >> I used following command to get the dt_recon work: >> >> Sampada$ export FREESURFER_HOME=/Applications/freesurfer >> Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /Applications/freesurfer >> FSFAST_HOME /Applications/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /Applications/freesurfer/subjects >> MNI_DIR /Applications/freesurfer/mni >> FSL_DIR /Applications/fsl >> Sampada$ tcsh >> Sampada% cd /Users/sampada/Desktop/DTIDCM/Raw/ >> ~/Desktop/DTIDCM/Raw] Sampada% setenv SUBJECTS_DIR >> /Users/Sampada/Desktop/DTIDCM/Raw >> ~/Desktop/DTIDCM/Raw] Sampada% set subj =Diff001 >> ~/Desktop/DTIDCM/Raw] Sampada% dt_recon --i >> /Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm --s $subj --o >> /Users/Sampada/Desktop/DTIDCM/Raw >> >> Error Message: ERROR: Flag >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm unrecognized. >> --i /Users/Sampada/Desktop/DTIDCM/Raw/I0005129.dcm >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005131.dcm >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005132.dcm >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005133.dcm >> /Users/Sampada/Desktop/DTIDCM/Raw/I0005134.dcm >> and so on? (dt_recon exited with ERRORS at Wed Feb 11 01:47:01 CST 2015) >> >> Then I used nii converted file instead of the dcm file and it shows >> the following error >> >> Sampada% dt_recon --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii >> --s $subj --o /Users/Sampada/Desktop/DTIDCM/Raw >> INFO: SUBJECTS_DIR is /Users/Sampada/Desktop/DTIDCM/Raw >> dt_recon logfile >> Wed Feb 11 15:02:47 CST 2015 >> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ >> setenv SUBJECTS_DIR /Users/Sampada/Desktop/DTIDCM/Raw >> cd /Users/Sampada/Desktop/DTIDCM/Raw >> /Applications/freesurfer/bin/dt_recon --i >> /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii --s Diff001 --o >> /Users/Sampada/Desktop/DTIDCM/Raw >> rmbp.home >> Sampada >> /Applications/fsl/bin/eddy_correct >> ECRefTP 0 >> #@#------------------------------- >> Converting input >> Wed Feb 11 15:02:47 CST 2015 >> cd /Users/Sampada/Desktop/DTIDCM/Raw >> mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii >> /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii >> mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii >> /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii... >> TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.994743, 0.0323186, 0.097165) >> j_ras = (0.0525116, 0.97562, 0.21309) >> k_ras = (0.0879093, -0.217072, 0.972189) >> writing to /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii... >> >> >> cd /Users/Sampada/Desktop/DTIDCM/Raw >> mri_probedicom --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii >> [rmbp:~/Desktop/DTIDCM/Raw] Sampada% >> >> I would be very grateful if I any response and know where I am going >> wrong. I am also attaching the dt_recon.log file with this query. >> >> Much thanks for your time! >> >> Kind regards, >> >> Sampada >> Post-Doctoral Associate >> University of Minnesota (East Bank) >> Molecular and neuroimaging laboratory >> Department of Psychiatry >> Minneapolis-55415 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150211_579c9922_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=1QGvGseTmDuMZx1v_EcVIcXGkIrmqNvF-q6iOIxvRPM&e= > > ------------------------------ > > Message: 5 > Date: Wed, 11 Feb 2015 18:01:53 -0500 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Interhemispheric registration of .mgh files > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54dbdf61.7000...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Probably easier to use mris_apply_reg, something like > > mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \ > --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \ > $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg > > mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi.rh.w-g.pct.mgh \ > --streg $SUBJECTS_DIR/$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg \ > $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg > > In the 2nd command line (for rh), lh.fsaverage_sym.sphere.reg is used. > This is intentional; the left hemis in the xhemi folder are actually > right hemis. > > doug > > > On 2/11/15 4:12 PM, Bruce Fischl wrote: >> Hi Konrad >> >> you should be able to do this with mri_surf2surf, although the syntax >> might be tricky. >> >> cheers >> Bruce >> On Mon, 9 Feb 2015, Konrad Wagstyl wrote: >> >>> Hi all, >>> >>> We're having some trouble using interhemispheric registration. It works >>> fine for files that are automatically registered eg thickness, volume etc. >>> but not for mgh files, like ?h.w-g.pct.mgh. >>> Is there a way of adding files to xhemi/surf/ so that other surfaces files >>> can be compared between hemispheres? >>> >>> Thanks, >>> Konrad >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >> >> > > > > ------------------------------ > > Message: 6 > Date: Wed, 11 Feb 2015 18:05:23 -0500 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Interhemispheric registration of .mgh files > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <54dbe033.6040...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > btw, to check, you can run this on the thicknesses and compare to what > you get with mris_preproc > > On 2/11/15 6:01 PM, Douglas Greve wrote: >> Probably easier to use mris_apply_reg, something like >> >> mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \ >> --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \ >> $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg >> >> mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi.rh.w-g.pct.mgh \ >> --streg $SUBJECTS_DIR/$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg \ >> $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg >> >> In the 2nd command line (for rh), lh.fsaverage_sym.sphere.reg is used. >> This is intentional; the left hemis in the xhemi folder are actually >> right hemis. >> >> doug >> >> >> On 2/11/15 4:12 PM, Bruce Fischl wrote: >>> Hi Konrad >>> >>> you should be able to do this with mri_surf2surf, although the syntax >>> might be tricky. >>> >>> cheers >>> Bruce >>> On Mon, 9 Feb 2015, Konrad Wagstyl wrote: >>> >>>> Hi all, >>>> >>>> We're having some trouble using interhemispheric registration. It works >>>> fine for files that are automatically registered eg thickness, volume etc. >>>> but not for mgh files, like ?h.w-g.pct.mgh. >>>> Is there a way of adding files to xhemi/surf/ so that other surfaces files >>>> can be compared between hemispheres? >>>> >>>> Thanks, >>>> Konrad >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >> >> > > > > ------------------------------ > > Message: 7 > Date: Thu, 12 Feb 2015 13:38:35 +1100 > From: Bronwyn Overs <b.ov...@neura.edu.au> > Subject: Re: [Freesurfer] Different results for GLM analysis of > parcellated regions and vertex-wise analyses > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <54dc122b.7080...@neura.edu.au> > Content-Type: text/plain; charset="windows-1252" > > Hi Doug, > > I am still trying to resolve the different results for GLMs completed in > Freesurfer and SPSS. Interestingly, I get the same p-values for each > method when I remove my continuous covariate (age) from the model > (leaving gender, group, and genderXgroup effects). This suggests that > the two methods are treating covariates in a different manner. > > Unfortunately, SPSS does allow you to print out the GLM design matrix or > use the design matrix from mri_glmfit as an input. However, I am able to > print out the contrast matrices for the analysis, which look like this: > > Contrast Intercept Age [Gender=Female] [Gender=Male] > [diagnosis=Case] [diagnosis=Control] [diagnosis=Case] * > [Gender=Female] [diagnosis=Case] * [Gender=Male] > [diagnosis=Control] * > [Gender=Female] [diagnosis=Control] * [Gender=Male] > Intercept 1 0 0.5 0.5 0.5 0.5 0.25 0.25 > 0.25 0.25 > Age 0 1 0 0 0 0 0 0 0 > 0 > gender 0 0 1 -1 0 0 0.5 -0.5 0.5 > -0.5 > diagnosis 0 0 0 0 1 -1 0.5 0.5 > -0.5 -0.5 > gender*diagnosis 0 0 0 0 0 0 1 > -1 -1 1 > > > While for mri_glmfit, the contrast vectors look like this: > > > Intercept Intercept Intercept Intercept Age > Slope Age Slope Age > Slope Age Slope > contrast Male-Case Female-Case Male-Control Female-Control > Male-Case Female-Case Male-Control Female-Control > age 0 0 0 0 0.5 0.5 0.5 0.5 > gender 0.5 -0.5 0.5 -0.5 0 0 0 0 > group 0.5 0.5 -0.5 -0.5 0 0 0 0 > gender*group 0.5 -0.5 -0.5 0.5 0 0 0 0 > > > From this information, do you know if there is a way to work out why > the two methods are producing different results when a continuous > covariate is included in the model? I am fairly stumped and would great > appreciate any further insight you can provide. > > Compared to > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 > > neura.edu.au > <https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= > > > > Follow @neuraustralia on twitter > <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= > >Follow NeuRA on facebook > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= > >Subscribe to the > NeuRA Magazine > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= > > > > On 9/02/2015 9:47 am, Bronwyn Overs wrote: >> Thanks. >> >> Kind regards, >> >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >> >> neura.edu.au >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >> > >> >> Follow @neuraustralia on twitter >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >> >Follow NeuRA on facebook >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >> >Subscribe to >> the NeuRA Magazine >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >> > >> >> On 7/02/2015 3:16 am, Douglas N Greve wrote: >>> It should be 10^-abs(sig) >>> >>> >>> On 02/06/2015 12:53 AM, Bronwyn Overs wrote: >>>> Hi Doug, >>>> >>>> Thanks for all of your help. I am investigating the differences >>>> between the design matrices now. >>>> >>>> I have one more query about the sig.table.dat file put out by the GLM >>>> using the parcellated ROIs. When I transform each of the values in >>>> this file to p values using 10^"value", some of the resulting p-value >>>> are >1. Do you know why this would be happening? Here is an example of >>>> one of my sig.table.dat files, where 10^.799 = 6.295: >>>> >>>> lh.aparc.thickness me_gender_ageRem me_group_ageRem >>>> lh_bankssts_thickness 0.107 -2.752 >>>> lh_caudalanteriorcingulate_thickness -2.616 -0.190 >>>> lh_caudalmiddlefrontal_thickness -0.701 -4.258 >>>> lh_cuneus_thickness 0.799 -1.178 >>>> lh_entorhinal_thickness 1.669 -4.129 >>>> lh_fusiform_thickness -0.088 -6.808 >>>> lh_inferiorparietal_thickness -0.665 -1.477 >>>> lh_inferiortemporal_thickness 0.149 -7.985 >>>> lh_isthmuscingulate_thickness -0.476 -2.393 >>>> lh_lateraloccipital_thickness 0.212 -1.189 >>>> lh_lateralorbitofrontal_thickness 0.288 -7.657 >>>> lh_lingual_thickness 1.148 -1.594 >>>> lh_medialorbitofrontal_thickness 1.405 -4.461 >>>> lh_middletemporal_thickness 0.727 -7.215 >>>> lh_parahippocampal_thickness -1.059 -2.854 >>>> lh_paracentral_thickness -0.514 -0.282 >>>> lh_parsopercularis_thickness 0.444 -3.541 >>>> lh_parsorbitalis_thickness -0.110 -7.075 >>>> lh_parstriangularis_thickness 0.244 -4.769 >>>> lh_pericalcarine_thickness 0.376 -0.218 >>>> lh_postcentral_thickness -0.485 -0.832 >>>> lh_posteriorcingulate_thickness -0.135 -1.241 >>>> lh_precentral_thickness 0.196 -2.102 >>>> lh_precuneus_thickness 0.018 -1.361 >>>> lh_rostralanteriorcingulate_thickness -1.208 -2.073 >>>> lh_rostralmiddlefrontal_thickness 0.437 -4.470 >>>> lh_superiorfrontal_thickness -0.141 -2.743 >>>> lh_superiorparietal_thickness -0.288 -0.365 >>>> lh_superiortemporal_thickness 0.227 -4.646 >>>> lh_supramarginal_thickness -1.185 -1.354 >>>> lh_frontalpole_thickness -0.325 -0.521 >>>> lh_temporalpole_thickness -0.067 -4.074 >>>> lh_transversetemporal_thickness -0.009 -1.618 >>>> lh_insula_thickness 0.553 -6.063 >>>> >>>> Kind regards, >>>> >>>> Bronwyn Overs >>>> Research Assistant >>>> >>>> Neuroscience Research Australia >>>> >>>> Neuroscience Research Australia >>>> Margarete Ainsworth Building >>>> Barker Street Randwick Sydney NSW 2031 Australia >>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>> >>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>> > >>>> >>>> Follow @neuraustralia on twitter >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>> >Follow NeuRA on facebook >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>> >Subscribe to >>>> the NeuRA >>>> Magazine<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>> > >>>> >>>> On 5/02/2015 10:46 am, Douglas N Greve wrote: >>>>> How sure are you that you are using the exact same model? Can you output >>>>> the design matrix from SPSS? Can you input the FS design matrix into >>>>> SPSS? Are you sure you are using the exact same input data? >>>>> >>>>> On 02/04/2015 06:32 PM, Bronwyn Overs wrote: >>>>>> Ahh right. I have just understood which part of the output I needed to >>>>>> look at. However, for the ROI GLM there are only 1-2 regions that were >>>>>> significantly different between groups, while the SPSS ANCOVA showed >>>>>> significant group differences for the majority of parcellated regions. >>>>>> I have confirmed that I am using the exact same model for each, so it >>>>>> is only the analysis method that differs. Do you know why these two >>>>>> methods would produce such disparate results? >>>>>> >>>>>> >>>>>> Kind regards, >>>>>> >>>>>> Bronwyn Overs >>>>>> Research Assistant >>>>>> >>>>>> Neuroscience Research Australia >>>>>> >>>>>> Neuroscience Research Australia >>>>>> Margarete Ainsworth Building >>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>> >>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>> > >>>>>> >>>>>> Follow @neuraustralia on twitter >>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>> >Follow NeuRA on facebook >>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>> >Subscribe to >>>>>> the NeuRA >>>>>> Magazine<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>> > >>>>>> >>>>>> On 5/02/2015 3:16 am, Douglas N Greve wrote: >>>>>>> I'm not sure that I understand what I'm looking at. If it is an ROI >>>>>>> analysis, then there is no surface, it should be about 40 numbers, one >>>>>>> for each ROI. >>>>>>> >>>>>>> On 02/03/2015 06:26 PM, Bronwyn Overs wrote: >>>>>>>> Hi Doug, >>>>>>>> >>>>>>>> Thanks for your correction. >>>>>>>> >>>>>>>> I have now completed the FDR for my case-control comparisons, and it >>>>>>>> appears that none of the regions survived. This is again quite >>>>>>>> confusing given the large number of parcellated regions that survived >>>>>>>> FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the >>>>>>>> sig.mgh file from ROI analysis looks as you would expect (it looks >>>>>>>> very strange to me): >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Kind regards, >>>>>>>> >>>>>>>> Bronwyn Overs >>>>>>>> Research Assistant >>>>>>>> >>>>>>>> Neuroscience Research Australia >>>>>>>> >>>>>>>> Neuroscience Research Australia >>>>>>>> Margarete Ainsworth Building >>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>> >>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>> > >>>>>>>> >>>>>>>> Follow @neuraustralia on twitter >>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>> >Follow NeuRA on facebook >>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>> >Subscribe to >>>>>>>> the NeuRA >>>>>>>> Magazine<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>> > >>>>>>>> >>>>>>>> On 4/02/2015 9:35 am, Douglas Greve wrote: >>>>>>>>> Yes, it should be .^ >>>>>>>>> >>>>>>>>> On 2/3/15 5:33 PM, Bronwyn Overs wrote: >>>>>>>>>> Hi Doug, >>>>>>>>>> >>>>>>>>>> I am having a problem with the line in Matlab 2014b: >>>>>>>>>> p = 10^-abs(sigmat); >>>>>>>>>> I keep getting the following error: >>>>>>>>>> Error using ^ >>>>>>>>>> Inputs must be a scalar and a square matrix. >>>>>>>>>> To compute elementwise POWER, use POWER (.^) >>>>>>>>>> instead. >>>>>>>>>> >>>>>>>>>> Do you know why this would be? >>>>>>>>>> >>>>>>>>>> Kind regards, >>>>>>>>>> >>>>>>>>>> Bronwyn Overs >>>>>>>>>> Research Assistant >>>>>>>>>> >>>>>>>>>> Neuroscience Research Australia >>>>>>>>>> >>>>>>>>>> Neuroscience Research Australia >>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>> >>>>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>>>> >Follow NeuRA on facebook >>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>>>> >Subscribe to >>>>>>>>>> the NeuRA >>>>>>>>>> Magazine<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> On 4/02/2015 2:22 am, Douglas Greve wrote: >>>>>>>>>>> There is not a way to do it from the command line. You can do it in >>>>>>>>>>> matlab, something like >>>>>>>>>>> >>>>>>>>>>> sig = MRIread('sig.mgh'); >>>>>>>>>>> sigmat = fast_vol2mat(sig); >>>>>>>>>>> p = 10^-abs(sigmat); >>>>>>>>>>> fdr = .05; >>>>>>>>>>> pthresh = fast_fdrthresh(p,fdr); >>>>>>>>>>> ind = find(p < pthresh); % This will be a list of ROI indices that >>>>>>>>>>> survive FDR >>>>>>>>>>> >>>>>>>>>>> doug >>>>>>>>>>> >>>>>>>>>>> On 2/2/15 10:26 PM, Bronwyn Overs wrote: >>>>>>>>>>>> Hi Doug, >>>>>>>>>>>> >>>>>>>>>>>> That makes perfect sense. Just one more thing then, how do you >>>>>>>>>>>> conduct an FDR via the command line for an ROI mri_glmfit analysis? >>>>>>>>>>>> >>>>>>>>>>>> Kind regards, >>>>>>>>>>>> >>>>>>>>>>>> Bronwyn Overs >>>>>>>>>>>> Research Assistant >>>>>>>>>>>> >>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>> >>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>>>> >>>>>>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>>>>>> > >>>>>>>>>>>> >>>>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>>>>>> >Follow NeuRA on facebook >>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>>>>>> >Subscribe >>>>>>>>>>>> to the NeuRA Magazine >>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>>>>>> > >>>>>>>>>>>> >>>>>>>>>>>> On 3/02/2015 2:00 pm, Douglas Greve wrote: >>>>>>>>>>>>> This is not something you would run the MC sim on because there >>>>>>>>>>>>> is no clustering, it is just a list of ROIs with their p-values. >>>>>>>>>>>>> The p-values are uncorrected. You can do bonferoni correction >>>>>>>>>>>>> across all the ROIs (or just the ones you are interested in). You >>>>>>>>>>>>> could do FDR too. >>>>>>>>>>>>> >>>>>>>>>>>>> doug >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 2/2/15 9:39 PM, Bronwyn Overs wrote: >>>>>>>>>>>>>> Thanks Doug, that worked well. >>>>>>>>>>>>>> >>>>>>>>>>>>>> However, is it possible to run a monte-carlo simulation with >>>>>>>>>>>>>> this GLM ROI analysis? I attempted to run it using the following >>>>>>>>>>>>>> command... >>>>>>>>>>>>>> mri_glmfit-sim --glmdir >>>>>>>>>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs >>>>>>>>>>>>>> --cwpvalthresh 0.05 --2spaces >>>>>>>>>>>>>> and received the following error: >>>>>>>>>>>>>> ERROR: could not determine file for >>>>>>>>>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir/mask >>>>>>>>>>>>>> >>>>>>>>>>>>>> Kind regards, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Bronwyn Overs >>>>>>>>>>>>>> Research Assistant >>>>>>>>>>>>>> >>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>> >>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>>>>>> >>>>>>>>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>>>>>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>>>>>>>> >Follow NeuRA on facebook >>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>>>>>>>> >Subscribe to >>>>>>>>>>>>>> the NeuRA Magazine >>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>>>>>>>>>>>>> On 3/02/2015 11:03 am, Douglas Greve wrote: >>>>>>>>>>>>>>> Even easier. Run aparcstats2table, then run mri_glmfit passing >>>>>>>>>>>>>>> the output of aparcstats2table with --table (instead of --y). >>>>>>>>>>>>>>> There's something on the wiki about it, also look for the ROI >>>>>>>>>>>>>>> tutorial. >>>>>>>>>>>>>>> doug >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 2/2/15 6:20 PM, Bronwyn Overs wrote: >>>>>>>>>>>>>>>> Hi Doug, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I am not sure how to run an ROI analysis using mri_glmfit. Is >>>>>>>>>>>>>>>> there a wiki page detailing this method (I was unable to find >>>>>>>>>>>>>>>> one)? Is the first step to map lh.aparc.label and >>>>>>>>>>>>>>>> rh.aparc.label from fsaverage to each of my individual >>>>>>>>>>>>>>>> subjects using mri_label2label? When I do so and then view the >>>>>>>>>>>>>>>> mapped label for an individual subject in freeview, it appears >>>>>>>>>>>>>>>> to be a continuous label for all of the parcellated regions >>>>>>>>>>>>>>>> combined. Is this correct? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Kind regards, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Bronwyn Overs >>>>>>>>>>>>>>>> Research Assistant >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>>>>>>>>>> >Follow NeuRA on facebook >>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>>>>>>>>>> >Subscribe >>>>>>>>>>>>>>>> to the NeuRA Magazine >>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On 3/02/2015 3:31 am, Douglas Greve wrote: >>>>>>>>>>>>>>>>> First, I would run the ROI analysis in mri_glmfit to see if >>>>>>>>>>>>>>>>> you get the same results as in SPSS. In the handfull of these >>>>>>>>>>>>>>>>> cases, no one has been able to correctly replicate the FS >>>>>>>>>>>>>>>>> design matrix in SPSS, so I suspect that is part of the >>>>>>>>>>>>>>>>> discrepancy. The other thing is that ROI and vertex-wise >>>>>>>>>>>>>>>>> analyses are simply different. As an extreme example, if some >>>>>>>>>>>>>>>>> of the vertices are pos and some are neg then they would >>>>>>>>>>>>>>>>> cancel out when you average them in an ROI but individually >>>>>>>>>>>>>>>>> could be significant at the vertex level. If you analyze the >>>>>>>>>>>>>>>>> average over the cluster then that should come out as >>>>>>>>>>>>>>>>> significant. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> doug >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On 2/1/15 11:36 PM, Bronwyn Overs wrote: >>>>>>>>>>>>>>>>>> Dear FreeSurfer Mailing List, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I have a sample of schizophrenia and control subjects for >>>>>>>>>>>>>>>>>> whom I have run a case-control analysis of cortical >>>>>>>>>>>>>>>>>> thickness using two separate methods (GLM vertex-wise >>>>>>>>>>>>>>>>>> analysis in freesurfer, repeated measures ANCOVA analysis of >>>>>>>>>>>>>>>>>> parcellated data in SPSS). However, for each methods of >>>>>>>>>>>>>>>>>> analysis I am getting extremely different results. For the >>>>>>>>>>>>>>>>>> GLM in Freesurfer I have only 1 small cluster in the frontal >>>>>>>>>>>>>>>>>> lobe that differs between cases and controls (controlling >>>>>>>>>>>>>>>>>> for all other IVs, FWMH = 10mm, cluster-forming threshold= >>>>>>>>>>>>>>>>>> .05, cluster-wise pval=.05), while for the ANCOVA method all >>>>>>>>>>>>>>>>>> but 8 of the parcellated regions differ significantly >>>>>>>>>>>>>>>>>> between groups (p<.05). For both methods I have used the >>>>>>>>>>>>>>>>>> same model of predictors (independent variables = gender, >>>>>>>>>>>>>>>>>> group, scanning site; covariate = age) and exactly the same >>>>>>>>>>>>>>>>>> sample of participants. I have also replicated the GLM >>>>>>>>>>>>>>>>>> analysis using the QDEC GUI to ensure that I had no made any >>>>>>>>>>>>>>>>>> mistakes. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Can you provide any insight into why I would be seeing such >>>>>>>>>>>>>>>>>> different results for each method using the same data set? >>>>>>>>>>>>>>>>>> My findings using the ANCOVA analysis make much more sense >>>>>>>>>>>>>>>>>> to me, given previous findings of reduced cortical thickness >>>>>>>>>>>>>>>>>> in schizophrenia subjects. I was surprised not to find the >>>>>>>>>>>>>>>>>> same pattern of effects using the GLM analysis. >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Kind regards, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Bronwyn Overs >>>>>>>>>>>>>>>>>> Research Assistant >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> neura.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__neura.edu.au&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VPnofuDjskMZzEWD86psAOv5hJ9nb_V6lRFxZlNh4Us&e= >>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_neuraustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=9jnjiUkQlmTzbqRnYQ9uCr_sxPPcHzrUAJM7nXLItKs&e= >>>>>>>>>>>>>>>>>> >Follow NeuRA on facebook >>>>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_NeuroscienceResearchAustralia&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=6wax-9uDwHa4fGcTXVlVgCnXQXN82VJNk-Gg7820FDg&e= >>>>>>>>>>>>>>>>>> >Subscribe >>>>>>>>>>>>>>>>>> to the NeuRA Magazine >>>>>>>>>>>>>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.neura.edu.au_help-2Dresearch_subscribe&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=A5NgAEIreXZ7yBIONn4_JUBKlogCpfQk4tEzkoYBXyY&e= >>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>>>>>>>>> person to whom it is >>>>>>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>>>>>>>>>> error and the e-mail >>>>>>>>>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>>>>>>>>> Compliance HelpLine at >>>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >>>>>>>>>>>>>>>>> . If the e-mail was sent to you in error >>>>>>>>>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>>>>>>>>> sender and properly >>>>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The information in this e-mail is intended only for the person >>>>>>>>>>>>>>> to whom it is >>>>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>>>>>>>>>>> and the e-mail >>>>>>>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>>>>>>> Compliance HelpLine at >>>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >>>>>>>>>>>>>>> . If the e-mail was sent to you in error >>>>>>>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>>>>>>> sender and properly >>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>>>>> whom it is >>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>>>>>>>>> and the e-mail >>>>>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>>>>> Compliance HelpLine at >>>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >>>>>>>>>>>>> . If the e-mail was sent to you in error >>>>>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>>>>> sender and properly >>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>>> whom it is >>>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>>>> the e-mail >>>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>>> Compliance HelpLine at >>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >>>>>>>>>>> . If the e-mail was sent to you in error >>>>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>>>> and properly >>>>>>>>>>> dispose of the e-mail. >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. 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If the e-mail was sent to you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> 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https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150212_f640a4f4_attachment-2D0007.png&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=p1Rld-oGyEq2fOnLck_N5-CgGNN_6R3GK9FJgqcx6nA&e= > > ------------------------------ > > Message: 8 > Date: Thu, 12 Feb 2015 04:03:53 +0000 > From: "Harms, Michael" <mha...@wustl.edu> > Subject: Re: [Freesurfer] updating from 5.0 to 5.3 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <d1018105.48b87%har...@psychiatry.wustl.edu> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150212_ddc368e1_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=m46wZvhZSYvUwj66fgWdJmOJg2tJmNDKpEJNLlr2GgI&e= > > ------------------------------ > > Message: 9 > Date: Thu, 12 Feb 2015 08:06:48 +0100 > From: "Thomas Potrusil" <am-dam-...@gmx.at> > Subject: Re: [Freesurfer] DTI question > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > > <trinity-a6639767-6d76-4724-8150-319cd16cc7d7-1423724808754@3capp-gmx-bs33> > > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20150212_fdbb63ff_attachment.html&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=EtKz_qUzha1voYMeyxmi6P3QlO5ZLVYQt9xJIOik03k&e= > > ------------------------------ > > Message: 10 > Date: Thu, 12 Feb 2015 11:31:09 +0000 > From: "Worker, Amanda" <amanda.wor...@kcl.ac.uk> > Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1423740669014.20...@kcl.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Anastasia, > > Apologies this looks like an error on my part. I had edited the script to > specify --init-spm instead of --init-fsl but forgot to specify that this > script was to be used. It all seems to be looking good now which is > fantastic- thanks very much for all of your help!! > > One last question, when using the command: > > freeview -tv > $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \ > -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & > > I am able to see all of the tracts clearly, except in some of the subjects > the Forceps Major seems to be missing. Changing the threshold doesn't seem to > make a difference. Do you have any ideas what the issue could be with this? > > Thanks, > > Amanda > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > Sent: 11 February 2015 16:21 > To: Freesurfer support list > Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] > > Hi Amanda - It doesn't look like the new registration was applied to the > aparc+aseg. Can you tell us the exact sequence of steps that you followed, > including your bbregister command line and the trac-all command lines that > you ran after running bbregister? > > Thanks, > a.y > > On Wed, 11 Feb 2015, Worker, Amanda wrote: > >> Hi, >> >> Thanks for this. --init-spm does appear to work and when checking the >> registration using the instructions bbregister gives it all looks good to >> me. However, when I check the dtifit_FA and aparc+aseg.bbr.nii it still >> doesn't look too good. I've continued on with the next steps for >> reconstructing the pathways just to see what happens, but they don't come >> out well. >> >> I've attached a screenshot of the registration using --init-spm and then >> also a screenshot of the dmri/dtfit_FA.nii.gz alone and with >> aparc+aseg.bbri.nii overlayed. >> >> Best wishes, >> >> Amanda >> >> >> >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> >> Sent: 06 February 2015 19:15 >> To: Bruce Fischl; Freesurfer support list >> Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] >> >> or --init-rr if you don't have matlab/spm >> >> On 02/06/2015 01:49 PM, Bruce Fischl wrote: >>> try --init-spm >>> On Fri, 6 Feb 2015, Anastasia Yendiki wrote: >>> >>>> >>>> Hi Amanda - So it looks like --init-header didn't work, and neither does >>>> --init-fsl. I'll defer to the father of bbregister, Doug, for clues >>>> about >>>> how to proceed. >>>> >>>> a.y >>>> >>>> On Wed, 21 Jan 2015, Worker, Amanda wrote: >>>> >>>>> Hi Anastasia, >>>>> >>>>> Yes I have done that. My command line was... " bbregister --s >>>>> PDPLUS010 --init-header --dti --mov >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz >>>>> --reg >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat >>>>> --fslmat >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat >>>>> " >>>>> >>>>> Following the instructions printed I can only see a tiny bit of the >>>>> dwi.nii.gz, as attached. >>>>> >>>>> I've also tried substituting --dti for --t1 in the command line and >>>>> that doesn't make much difference. >>>>> >>>>> Do you have any other ideas? >>>>> >>>>> Thanks, >>>>> >>>>> Amanda >>>>> >>>>> >>>>> >>>>> >>>>> ________________________________________ >>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia >>>>> Yendiki <ayend...@nmr.mgh.harvard.edu> >>>>> Sent: 15 January 2015 15:36 >>>>> To: Freesurfer support list >>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>> >>>>> Did you follow the instructions and the end of the output of the >>>>> bbregister command? What does that look like? See what I wrote below >>>>> about >>>>> looking for the bbregister command in trac-all.log, running it >>>>> separately >>>>> on one subject after changing that one option and looking at its >>>>> output. >>>>> >>>>> On Wed, 14 Jan 2015, Worker, Amanda wrote: >>>>> >>>>>> Sorry, I misunderstood. >>>>>> >>>>>> I've attached a screenshot of what I can see, it does look like >>>>>> there is probably a different problem now as both the >>>>>> dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Amanda >>>>>> >>>>>> >>>>>> ________________________________________ >>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia >>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu> >>>>>> Sent: 13 January 2015 17:52 >>>>>> To: Freesurfer support list >>>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>>> >>>>>> It's impossible to know unless you actually check the registration. >>>>>> See my >>>>>> previous email below on how to do that. >>>>>> >>>>>> On Tue, 13 Jan 2015, Worker, Amanda wrote: >>>>>> >>>>>>> I have edited the trac-preproc script to "--init-header" instead >>>>>>> of "--init-fsl" - hoping that this would fix the registration >>>>>>> problem. Perhaps this hasn't helped? >>>>>>> ________________________________________ >>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia >>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu> >>>>>>> Sent: 12 January 2015 19:58 >>>>>>> To: Freesurfer support list >>>>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>>>> >>>>>>> Have you checked that the registration has been fixed? It looks >>>>>>> like it >>>>>>> might not. >>>>>>> >>>>>>> On Mon, 12 Jan 2015, Worker, Amanda wrote: >>>>>>> >>>>>>>> Yes of course. Please find attached. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Amanda >>>>>>>> ________________________________________ >>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia >>>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu> >>>>>>>> Sent: 12 January 2015 16:39 >>>>>>>> To: Freesurfer support list >>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>>>>> >>>>>>>> Can you please attach the entire trac-all.log file? It's hard to >>>>>>>> tell just >>>>>>>> from the last few lines, the initial error may have happened much >>>>>>>> earlier. >>>>>>>> >>>>>>>> On Mon, 12 Jan 2015, Worker, Amanda wrote: >>>>>>>> >>>>>>>>> Hi Anastasia, >>>>>>>>> >>>>>>>>> Thank you for your response. I have made the changes that you >>>>>>>>> recommended and attempted to run trac-all -prep on one of the >>>>>>>>> subjects with errors. I am now getting the following error: >>>>>>>>> >>>>>>>>> Writing output files to >>>>>>>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* >>>>>>>>> Writing spline volumes to >>>>>>>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz >>>>>>>>> Segmentation fault >>>>>>>>> >>>>>>>>> trac-preproc-edit exited with ERRORS at Fri Jan >>>>>>>>> >>>>>>>>> >>>>>>>>> Do you have any idea what the problem could be now? >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Amanda >>>>>>>>> >>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia >>>>>>>>> Yendiki [ayend...@nmr.mgh.harvard.edu] >>>>>>>>> Sent: 07 January 2015 17:11 >>>>>>>>> To: Freesurfer support list >>>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>>>>>> >>>>>>>>> Hi Amanda - See attached screenshot of your data, there is a gross >>>>>>>>> misregistration (~45 degree angle rotation) between the >>>>>>>>> diffusion and >>>>>>>>> anatomical. You can check if this is the case for the rest of >>>>>>>>> your bad >>>>>>>>> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and >>>>>>>>> anatomical >>>>>>>>> segmentation mapped to diffusion space >>>>>>>>> (dlabel/diff/aparc+aseg.bbr.nii). >>>>>>>>> >>>>>>>>> According to bbregister czar Doug, a big error like this in >>>>>>>>> bbregister >>>>>>>>> happens when the initialization of the registration fails. If the >>>>>>>>> diffusion and T1 were acquired in the same session, you can try >>>>>>>>> initializing the registration from the headers of the images, by >>>>>>>>> running >>>>>>>>> bbregister with "--init-header" instead of "--init-fsl". >>>>>>>>> >>>>>>>>> You can try it on one of your subjects first. Search for the >>>>>>>>> bbregister >>>>>>>>> command line in trac-all.log of this subject and rerun >>>>>>>>> bbregister with the >>>>>>>>> changed option. Follow the instructions that bbregister prints >>>>>>>>> out when >>>>>>>>> it's done to check the registration. >>>>>>>>> >>>>>>>>> To change how tracula does this, you'll have to edit the script >>>>>>>>> $FREESURFER_HOME/bin/trac-preproc >>>>>>>>> Search for "bbregister" and edit the --init-fsl option. Then rerun >>>>>>>>> trac-all for the subjects that had this problem. You can skip >>>>>>>>> the first 2 >>>>>>>>> steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa. >>>>>>>>> >>>>>>>>> Hope this helps, >>>>>>>>> a.y >>>>>>>>> >>>>>>>>> PS: Yes, when you send something with filedrop that I should >>>>>>>>> look at, give >>>>>>>>> my email address as the recipient. >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, 7 Jan 2015, Worker, Amanda wrote: >>>>>>>>> >>>>>>>>>> Hi Anastasia, >>>>>>>>>> >>>>>>>>>> Thanks for your response. I have sent over a zip file via the >>>>>>>>>> filedrop >>>>>>>>>> portal, it seemed to fail each time I tried to send it to >>>>>>>>>> freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email >>>>>>>>>> address - hopefully you have received this. >>>>>>>>>> >>>>>>>>>> I've had a look at the segmentations and they look ok, so I >>>>>>>>>> think there >>>>>>>>>> may be an issue with registrating between the T1 and diffusion. >>>>>>>>>> Anyway I >>>>>>>>>> have sent an example over, hopefully this will give you some >>>>>>>>>> idea of >>>>>>>>>> what has gone wrong. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Amanda >>>>>>>>>> >>>>>>>>>> ________________________________________ >>>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia >>>>>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu> >>>>>>>>>> Sent: 11 December 2014 19:37 >>>>>>>>>> To: Freesurfer support list >>>>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error >>>>>>>>>> >>>>>>>>>> Hi Amanda - The final masks used by tracula are derived from the >>>>>>>>>> structural and not the diffusion data, i.e., they are the >>>>>>>>>> whole-brain >>>>>>>>>> FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto >>>>>>>>>> diffusion >>>>>>>>>> space and dilated slightly. It may be that there was something >>>>>>>>>> wrong with >>>>>>>>>> the FreeSurfer reconstructions of those subjects (if, for >>>>>>>>>> example, the T1 >>>>>>>>>> contrast was poorer in part of the brain and the part was not >>>>>>>>>> included in >>>>>>>>>> the brain mask), or that there was misregistration between the >>>>>>>>>> T1 and >>>>>>>>>> diffusion. You can troubleshoot this by looking at the >>>>>>>>>> aparc+aseg in >>>>>>>>>> diffusion space (from the dlabel/diff directory, over the FA >>>>>>>>>> map (from the >>>>>>>>>> dmri directory). >>>>>>>>>> >>>>>>>>>> If you still have trouble deciding what went wrong, you can >>>>>>>>>> upload a zip >>>>>>>>>> file for me with all the directories created by trac-all (dmri, >>>>>>>>>> dlabel, >>>>>>>>>> etc) for one of these subjects, here: >>>>>>>>>> >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2_&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=-niii2hyPI9_6kgSmcwH62QFRrqZ648V-V-NIEn57Q4&e= >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> a.y >>>>>>>>>> >>>>>>>>>> On Thu, 27 Nov 2014, Worker, Amanda wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Dear All, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I have run all of the pre-processing steps on my DTI data and >>>>>>>>>>> as I am >>>>>>>>>>> checking my nodif_brain_mask I have realised that some of the >>>>>>>>>>> masks have >>>>>>>>>>> become distorted and twisted in some way. I have attached >>>>>>>>>>> screenshots of >>>>>>>>>>> both the raw data (which looks fine) and the white mask (which is >>>>>>>>>>> distorted). In addition, as I have read that it is important >>>>>>>>>>> to check the >>>>>>>>>>> dtifit_V1 and dtifit_FA I have also included these in the word >>>>>>>>>>> document, >>>>>>>>>>> incase this helps. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> This distortion has occured for approximately a quarter of the >>>>>>>>>>> subjects that >>>>>>>>>>> I have processed and the rest look good. Please can you let me >>>>>>>>>>> know if you >>>>>>>>>>> have any ideas about what has gone wrong and how to fix this? >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thanks in advance for your help, >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Amanda >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person >>>>>>>>>> to whom it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>>>>>> and the e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>> Compliance HelpLine at >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >>>>>>>>>> . If the e-mail was sent >>>>>>>>>> to you in error >>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>> sender and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>> >>>> >>>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=VnY1uRHei5_njvGn2gHcftHpE9IQv50RrOCUxPEm9vw&e= >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=UkXAjuoKAJsC3KcgGNKYKWQryTNh_Cov2uzll3GTd_w&e= >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > > > ------------------------------ > > Message: 11 > Date: Thu, 12 Feb 2015 15:24:02 +0000 > From: Konrad Wagstyl <kw...@cam.ac.uk> > Subject: Re: [Freesurfer] Interhemispheric registration of .mgh files > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <e2101436-5fd6-4046-bdb1-dbb7cc15a...@cam.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Thanks. The mris_apply_reg works like a charm. Just to clarify for anyone > interested, these commands register both left and right .mgh files to lh > fsaverage_sym. > > Cheers, > Konrad > >> On 11 Feb 2015, at 23:05, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: >> >> btw, to check, you can run this on the thicknesses and compare to what >> you get with mris_preproc >> >> On 2/11/15 6:01 PM, Douglas Greve wrote: >>> Probably easier to use mris_apply_reg, something like >>> >>> mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \ >>> --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \ >>> $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg >>> >>> mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi.rh.w-g.pct.mgh \ >>> --streg $SUBJECTS_DIR/$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg \ >>> $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg >>> >>> In the 2nd command line (for rh), lh.fsaverage_sym.sphere.reg is used. >>> This is intentional; the left hemis in the xhemi folder are actually >>> right hemis. >>> >>> doug >>> >>> >>> On 2/11/15 4:12 PM, Bruce Fischl wrote: >>>> Hi Konrad >>>> >>>> you should be able to do this with mri_surf2surf, although the syntax >>>> might be tricky. >>>> >>>> cheers >>>> Bruce >>>> On Mon, 9 Feb 2015, Konrad Wagstyl wrote: >>>> >>>>> Hi all, >>>>> >>>>> We're having some trouble using interhemispheric registration. It works >>>>> fine for files that are automatically registered eg thickness, volume >>>>> etc. but not for mgh files, like ?h.w-g.pct.mgh. >>>>> Is there a way of adding files to xhemi/surf/ so that other surfaces >>>>> files can be compared between hemispheres? >>>>> >>>>> Thanks, >>>>> Konrad >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=SdG3MAsjgOL6ubQPYstixwLSuixPqsV0Mk6s8Iqpl_4&e= >> . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=AwICAg&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=UhsLycigCHMsEqakbi9FEaSyxA12muzKL7XCcvWFgCQ&s=pIyr-W-cl8jY4gW5Yj7jpWfKt5YF4ZQJfDKHCV5ilSQ&e= > > End of Freesurfer Digest, Vol 132, Issue 15 > ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
